RAVE Preprocess: Notch Filter
subject <- raveio::RAVESubject$new(
project_name = project_name,
subject_code = subject_code,
strict = FALSE
)imported_electrodes <- subject$electrodes[
subject$preprocess_settings$data_imported
]
if(!length(imported_electrodes)){
stop("The subject exists but its signal has not been imported yet.")
}
lb <- unlist(notch_filter_lowerbound)
ub <- unlist(notch_filter_upperbound)
if(length(lb) != length(ub)) {
stop(sprintf("Notch filter lower bound length should match with the upper bound length (%d vs %d)", length(lb), length(ub)))
}
if(length(lb)) {
if(!all(lb < ub)) {
sel <- lb >= ub
lb <- lb[sel]
ub <- ub[sel]
stop("Notch filter lower bounds must be uniformly smaller than the upper bounds: (", paste0(lb, ">", ub, collapse = ", "), ")")
}
}
filter_settings <- list(
lb = lb,
ub = ub,
domain = 1
)
blocks <- subject$preprocess_settings$blocks
electrodes <- imported_electrodes
filters <- filter_settings
fmt <- file.path(subject$preprocess_path, "voltage", "electrode_%d.h5")
sample_rates <- subject$raw_sample_rates
sample_rates <- sapply(electrodes, function(e){
sample_rates[subject$electrodes == e]
})
dipsaus::lapply_async2(
seq_along(electrodes), function(ii){
e <- electrodes[[ii]]
srate <- sample_rates[[ii]]
h5_path <- sprintf(fmt, e)
h5_names <- gsub("^/", "", raveio::h5_names(h5_path))
sel <- sprintf("raw/%s", blocks) %in% h5_names
if(!all(sel)) {
stop(sprintf(
"Cannot find imported block(s): %s (electrode %s)",
blocks[!sel], e
))
}
for(block in blocks){
cat(block, e, "\n")
signal <- raveio::load_h5(h5_path, sprintf("raw/%s", block), ram = TRUE)
signal <- ravetools::notch_filter(s = signal, sample_rate = srate, lb = filters$lb, ub = filters$ub, domain = filters$domain)
raveio::save_h5(x = signal, file = h5_path, name = sprintf("notch/%s", block), chunk = 1024, replace = TRUE, ctype = "numeric")
}
}, plan = FALSE, callback = function(ii){
sprintf("Applying Notch filters|Electrode - %s", electrodes[[ii]])
}
)
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# save to subject
preproc <- raveio::RAVEPreprocessSettings$new(subject = subject$subject_id)
for(e in electrodes){
preproc$data[[as.character(e)]]$notch_filtered <- TRUE
}
preproc$save()
apply_notch <- list(
electrodes = electrodes,
notch_filter_lowerbound = filters$lb,
notch_filter_upperbound = filters$ub,
timestamp = strftime(Sys.time(), usetz = TRUE)
)
subject$set_default(
namespace = "notch_filter",
key = "parameters",
value = apply_notch
)
diagnostic_plots <- FALSE
params <- as.list(diagnostic_plot_params)
background <- params$background
foreground <- params$foreground
if(!length(background) == 1) {
background <- "white"
}
if(!length(foreground) == 1) {
foreground <- "black"
}
if(length(params$path) == 1) {
grDevices::pdf(file = params$path, width = 12, height = 7, onefile = TRUE, bg = background, fg = foreground, useDingbats = FALSE)
on.exit({
grDevices::dev.off()
}, add = TRUE)
}
winlen <- as.numeric(params$window_length)
if(!length(winlen) || is.na(winlen)) {
winlen <- "auto"
}
max_freq <- as.numeric(params$max_frequency)
if(!length(max_freq) || is.na(max_freq)) {
max_freq <- 300
}
nbins <- as.numeric(params$histogram_bins)
if(!length(nbins) || is.na(nbins)) {
nbins <- 50
}
font_size <- as.numeric(params$font_size)
if(!length(font_size) || is.na(font_size)) {
font_size <- 2
}
quiet <- isTRUE(params$quiet)
source("./R/diagnose_plot.R", local = TRUE)
diagnostic_plots <- diagnose_notch_filters(
subject = subject,
electrodes = imported_electrodes,
max_freq = max_freq,
winlen = winlen,
nbins = nbins,
bg = background,
fg = foreground,
cex = font_size,
std = 3,
lwd = 0.3,
mar = c(5.2, 5.1, 4.1, 2.1), mai = c(0.6, 0.6, 0.4, 0.1),
quiet = quiet
)
#> [Generating diagnostic plots]: initializing...
[Generating diagnostic plots]: Electrode 14 (start) (1 out of 24) 
#> [Generating diagnostic plots]: Electrode 14 (end) (2 out of 24)
[Generating diagnostic plots]: Electrode 15 (start) (3 out of 24) 
#> [Generating diagnostic plots]: Electrode 15 (end) (4 out of 24)
[Generating diagnostic plots]: Electrode 16 (start) (5 out of 24) 
#> [Generating diagnostic plots]: Electrode 16 (end) (6 out of 24)
[Generating diagnostic plots]: Electrode 17 (start) (7 out of 24) 
#> [Generating diagnostic plots]: Electrode 17 (end) (8 out of 24)
[Generating diagnostic plots]: Electrode 18 (start) (9 out of 24) 
#> [Generating diagnostic plots]: Electrode 18 (end) (10 out of 24)
[Generating diagnostic plots]: Electrode 19 (start) (11 out of 24) 
#> [Generating diagnostic plots]: Electrode 19 (end) (12 out of 24)
[Generating diagnostic plots]: Electrode 20 (start) (13 out of 24) 
#> [Generating diagnostic plots]: Electrode 20 (end) (14 out of 24)
[Generating diagnostic plots]: Electrode 21 (start) (15 out of 24) 
#> [Generating diagnostic plots]: Electrode 21 (end) (16 out of 24)
[Generating diagnostic plots]: Electrode 22 (start) (17 out of 24) 
#> [Generating diagnostic plots]: Electrode 22 (end) (18 out of 24)
[Generating diagnostic plots]: Electrode 23 (start) (19 out of 24) 
#> [Generating diagnostic plots]: Electrode 23 (end) (20 out of 24)
[Generating diagnostic plots]: Electrode 24 (start) (21 out of 24) 
#> [Generating diagnostic plots]: Electrode 24 (end) (22 out of 24)
[Generating diagnostic plots]: Electrode 25 (start) (23 out of 24) 
#> [Generating diagnostic plots]: Electrode 25 (end) (24 out of 24) Build, Visualize, & Run
Please make sure the following code block is at the end of your pipeline file. This block will build the pipeline and generate a make-notch_filter.R script with your pipeline markdown file. RAVE will use the generated pipeline script to execute the pipeline in the dashboard application, or in massive production mode.
Once the pipeline script make-notch_filter.R is built, you can visualize and execute the pipeline without the need of re-knit this document. Notice we use r block instead of rave. (This is because the code blocks are not part of pipeline targets.)
Sys.setenv("RAVE_PIPELINE" = normalizePath("."))
raveio::pipeline_run(type = "vanilla")
#> • start target settings_path
#> • built target settings_path
#> • start target settings
#> • built target settings
#> • start target notch_filter_lowerbound
#> • built target notch_filter_lowerbound
#> • start target notch_filter_upperbound
#> • built target notch_filter_upperbound
#> ✓ skip target diagnostic_plot_params
#> ✓ skip target subject_code
#> ✓ skip target project_name
#> • start target filter_settings
#> • built target filter_settings
#> • start target subject
#> • built target subject
#> • start target imported_electrodes
#> • built target imported_electrodes
#> • start target diagnostic_plots
#> [Generating diagnostic plots]: initializing...
[Generating diagnostic plots]: Electrode 14 (start) (1 out of 24)
#> [Generating diagnostic plots]: Electrode 14 (end) (2 out of 24)
[Generating diagnostic plots]: Electrode 15 (start) (3 out of 24)
#> [Generating diagnostic plots]: Electrode 15 (end) (4 out of 24)
[Generating diagnostic plots]: Electrode 16 (start) (5 out of 24)
#> [Generating diagnostic plots]: Electrode 16 (end) (6 out of 24)
[Generating diagnostic plots]: Electrode 17 (start) (7 out of 24)
#> [Generating diagnostic plots]: Electrode 17 (end) (8 out of 24)
[Generating diagnostic plots]: Electrode 18 (start) (9 out of 24)
#> [Generating diagnostic plots]: Electrode 18 (end) (10 out of 24)
[Generating diagnostic plots]: Electrode 19 (start) (11 out of 24)
#> [Generating diagnostic plots]: Electrode 19 (end) (12 out of 24)
[Generating diagnostic plots]: Electrode 20 (start) (13 out of 24)
#> [Generating diagnostic plots]: Electrode 20 (end) (14 out of 24)
[Generating diagnostic plots]: Electrode 21 (start) (15 out of 24)
#> [Generating diagnostic plots]: Electrode 21 (end) (16 out of 24)
[Generating diagnostic plots]: Electrode 22 (start) (17 out of 24)
#> [Generating diagnostic plots]: Electrode 22 (end) (18 out of 24)
[Generating diagnostic plots]: Electrode 23 (start) (19 out of 24)
#> [Generating diagnostic plots]: Electrode 23 (end) (20 out of 24)
[Generating diagnostic plots]: Electrode 24 (start) (21 out of 24)
#> [Generating diagnostic plots]: Electrode 24 (end) (22 out of 24)
[Generating diagnostic plots]: Electrode 25 (start) (23 out of 24)
#> [Generating diagnostic plots]: Electrode 25 (end) (24 out of 24)
#> • built target diagnostic_plots
#> • start target apply_notch
#> 008 14
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#> 008 18
#> 008 19
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#> • built target apply_notch
#> • end pipeline
#> <Pipeline result container>
#> process: native
#> status: running (0 of 12)
raveio::pipeline_progress(method = 'details')
#> # A tibble: 12 × 2
#> name progress
#> <chr> <chr>
#> 1 settings_path built
#> 2 settings built
#> 3 notch_filter_lowerbound built
#> 4 notch_filter_upperbound built
#> 5 diagnostic_plot_params skipped
#> 6 subject_code skipped
#> 7 project_name skipped
#> 8 filter_settings built
#> 9 subject built
#> 10 imported_electrodes built
#> 11 diagnostic_plots built
#> 12 apply_notch built